2008 Student Research Conference:
21st Annual Student Research Conference

Molecular Dynamics Studies of Human Immunodeficiency Virus RSG-1.2-RRE Recognition
Lauren A. Michael
Dr. Maria Nagan, Faculty Mentor

Recognition of the human immunodeficiency virus (HIV) Rev responsive element (RRE) RNA by the Rev protein is an essential step in the viral life cycle. A synthetic peptide, RSG-1.2, recognizes RRE with greater affinity and specificity than the native Rev peptide. Molecular dynamics (MD) simulations of the RSG-1.2-RRE complex have been performed under four salt concentrations in the presence of explicit solvent (~72,000-79,000 total atoms) with AMBER 8.0. Each trajectory was equilibrated for 10.0 ns prior to collection of statistics for an additional 10.0 ns. Intermolecular hydrogen bonding has been extensively analyzed, and important arginine residues in RSG-1.2 have been specifically evaluated. Structural calculations have been performed to examine the conformation of RSG-1.2 and its position relative to the RRE. Data demonstrate that the RSG-1.2 position is very stable as a result of its unique conformation, hydrogen bonding, and the presence of specific hydrophobic interactions not observed in Rev-RRE recognition.

Keywords: simulation, RNA, protein, hydrogen bond, HIV, RRE, RSG-1.2, Rev

Topic(s):Chemistry

Presentation Type: Oral Paper

Session: 44-4
Location: VH 1320
Time: 3:30

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